For certain diseases linked to autosomal dominant inheritance of genetic mutations, doctors are now able to improve medical treatment for affected people, even before clinical presentation of symptoms, due to molecular diagnosis of the heritable mutation. Some diseases that result from such heritable mutations are hereditary breast and ovarian cancer, hereditary hemorrhagic telangiectasia, cystic fibrosis, colorectal cancer and retinoblastoma.
For example, molecular diagnosis requires a comparison of patient DNA to “wild type” DNA accepted by a consensus of experts as normal. Some general classes of mutations that cause disease include deletion of all or part of a critical gene, insertions and duplications of isolated portions of DNA, and hypermethylation of gene promoter regions. In some diseases, certain genetic mutations are found to recur in the DNA of many patients, the same type of mutations at the same locations in DNA, across many individuals.
For example, in both Duchenne Muscular Dystrophy and Becker Muscular Dystrophy, mutations cluster in two recombination “hot spots”. (Den Dunnen et al 1989). Similarly, the most common genetic defect that causes cystic fibrosis (ΔF508) accounts for about 30-80% of mutant alleles depending on the ethnic group [CF Genotype-Phenotype Consortium1993]
More typically, however, heritable diseases are linked to mutations that do not recur with great frequency across affected families. Before any beneficial change in treatment can be offered to families affected by such a disease, first it is necessary to search the DNA for the mutation(s) that cause disease. Once the familial mutation is identified, all individuals at risk can be tested to see if they carry the mutation and beneficial changes can often be made to the surveillance or treatment of affected individuals.
The prior art in searching for genetic mutations relies first on PCR amplification and sequencing of DNA from genes linked to particular diseases. For some diseases, it is known to be cost-effective to use other preliminary screening techniques to detect the existence of a mutation and to restrict the search for sequencing errors to a smaller region of DNA. Examples of such supplementary techniques include Quantitative Multiplex PCR (QMPCR), Single Stranded Conformational Polymorphism (SSCP) analysis, and heteroduplex analysis.
Because many genetic diseases are linked to a multiplicity of genetic mutations, if molecular diagnosis is to achieve high levels of sensitivity, the analysis must involve multiple medical diagnostic assays. Although the prior art recognizes the value of multiple hierarchical assays, there is no discussion in the relevant literature to explain how one should order multiple medical diagnostic assays to achieve the shortest possible turnaround time, the lowest possible test costs, or both.
Cost effective health care requires that a molecular test methodology be shown to be sensitive, accurate and economically feasible before it becomes routine clinical care. Therefore, it is of significant economic value to health care providers that molecular test strategies are designed to provide the highest sensitivity to mutations, yet at the lowest possible cost and in the least possible time. The current invention makes such design capacity available to knowledgeable users.